There's minimal overlap between the comic book reading audience and the movie-going public. Stopping publication of X Men books would cut off a small, but steady revenue stream for Disney/Marvel and upset loyal readers without having any impact on movie rights.

Disney controls the merchandise rights for the X-Men films, so you won't see the shelves stacked with merchandise or the valuable corporate tie-ins we've seen in the MCU films and Man of Steel. The X films peaked back in 2006, and Disney/Marvel's best play is to hope the box office drop continues with The Wolverine (I think it will), and that Days of Future Past doesn't revitalize the franchise.

the only problem is that Fox (through a rep) has stated that if the x-men movies start to lose money, they would make a low budget movie, show it in 1 theater and then send it to home video just to maintain the rights. which is just dirty. now if Disney did kill them off in comics, they could weather the loss, without x-men comics, Disney will be just fine. The fan backlash would be directed at Disney at first, but would eventually fall on Fox and I believe they would cave.